Alignments for a candidate for ilvI in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Dechlorosoma suillum PS

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate Dsui_3529 Dsui_3529 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-18810
         (585 letters)



>FitnessBrowser__PS:Dsui_3529
          Length = 566

 Score =  803 bits (2075), Expect = 0.0
 Identities = 398/568 (70%), Positives = 473/568 (83%), Gaps = 5/568 (0%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           + GAEI++  L EE V+YV+GYPGG+VL+IYDEL KQ   +HILVRHEQAAVHAAD Y+R
Sbjct: 3   LTGAEIVIRCLQEEKVDYVFGYPGGSVLHIYDELFKQDDIKHILVRHEQAAVHAADAYSR 62

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           ++ +VGVALVTSGPGVTNAVTGIATAY+DSIPMVV+ G VPT+ IGQDAFQECDTVGITR
Sbjct: 63  SSERVGVALVTSGPGVTNAVTGIATAYMDSIPMVVLCGQVPTYYIGQDAFQECDTVGITR 122

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198
           P VKHNFLVKDV+DLA+T+KKAF IA TGRPGPVVVDIPKD++ N C++EYP S+ MRSY
Sbjct: 123 PCVKHNFLVKDVKDLASTMKKAFHIAKTGRPGPVVVDIPKDITANKCEFEYPASVQMRSY 182

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLG 258
           NPV KGH GQI+KAV +L  A++P IYTGGGVVL++AS++L +LA     PVTNTLMGLG
Sbjct: 183 NPVVKGHLGQIKKAVQMLLEAKQPIIYTGGGVVLSDASEKLVKLAKRLNFPVTNTLMGLG 242

Query: 259 AFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHID 318
            +P T KQFVGMLGMHGTYEANM MQ+ DV++AIGARFDDRVIGNP HF    RKIIH+D
Sbjct: 243 GYPATDKQFVGMLGMHGTYEANMTMQHADVVLAIGARFDDRVIGNPEHFGGVPRKIIHVD 302

Query: 319 IDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLK 378
           IDPSSISKRVKVD+PIVGNV DVL EL+  +   D       ++ WW+QI+ WR+ + L 
Sbjct: 303 IDPSSISKRVKVDVPIVGNVPDVLDELLKLL--DDGAKAAPDVSDWWQQIDGWRAKNSLG 360

Query: 379 YDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMG 438
           Y +  ++I+PQYVVEK++E+T+G+AFI SDVGQHQM+AAQ+YKFD+PRRWINSGGLGTMG
Sbjct: 361 Y-KQGDLIEPQYVVEKLYEVTQGEAFITSDVGQHQMFAAQYYKFDKPRRWINSGGLGTMG 419

Query: 439 VGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQW 498
           VGLPYAMG+  A P  +V  ITGEGSIQMCIQELSTC Q++ PVKI +LNNG LGMVRQW
Sbjct: 420 VGLPYAMGVLFANPGAQVACITGEGSIQMCIQELSTCKQFELPVKIINLNNGMLGMVRQW 479

Query: 499 QEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF-RLKDRTVFLDF 557
           QE+ Y  RYS SY+ +LPDFVKLAE+YGHVGMR+EK  DV PAL++AF   KDR VF+DF
Sbjct: 480 QEMFYSKRYSQSYVTSLPDFVKLAESYGHVGMRIEKPEDVVPALKKAFTEYKDRLVFMDF 539

Query: 558 QTDPTENVWPMVQAGKGISEMLLGAEDL 585
             DP  NV+PMV AGKG+SEM+L +EDL
Sbjct: 540 IIDPEANVYPMVAAGKGLSEMIL-SEDL 566


Lambda     K      H
   0.319    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1016
Number of extensions: 38
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 585
Length of database: 566
Length adjustment: 36
Effective length of query: 549
Effective length of database: 530
Effective search space:   290970
Effective search space used:   290970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate Dsui_3529 Dsui_3529 (acetolactate synthase, large subunit, biosynthetic type)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.16524.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.8e-253  826.9   1.2   4.4e-253  826.7   1.2    1.0  1  lcl|FitnessBrowser__PS:Dsui_3529  Dsui_3529 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3529  Dsui_3529 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  826.7   1.2  4.4e-253  4.4e-253       1     556 [.       3     563 ..       3     564 .. 0.97

  Alignments for each domain:
  == domain 1  score: 826.7 bits;  conditional E-value: 4.4e-253
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+gaei+++ l++e+v++vfGyPGG+vl+iyd+l+ +++++hilvrheqaa+haad y+r+s +vGv+l+tsGPG t
  lcl|FitnessBrowser__PS:Dsui_3529   3 LTGAEIVIRCLQEEKVDYVFGYPGGSVLHIYDELFkQDDIKHILVRHEQAAVHAADAYSRSSERVGVALVTSGPGVT 79 
                                       68*********************************999*************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n+vtgiatay+ds+P+vvl Gqv+t  iG+dafqe+d +Git+p++kh+flvk+++dl++++k+af+ia+tGrPGPv
  lcl|FitnessBrowser__PS:Dsui_3529  80 NAVTGIATAYMDSIPMVVLCGQVPTYYIGQDAFQECDTVGITRPCVKHNFLVKDVKDLASTMKKAFHIAKTGRPGPV 156
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkip 230
                                       +vd+Pkd+t++++e+e++++v++++y+p vkgh  qikka++++ +ak+P+++ GgGv+ ++ase+l++la+rl+ p
  lcl|FitnessBrowser__PS:Dsui_3529 157 VVDIPKDITANKCEFEYPASVQMRSYNPVVKGHLGQIKKAVQMLLEAKQPIIYTGGGVVLSDASEKLVKLAKRLNFP 233
                                       ***************************************************************************** PP

                         TIGR00118 231 vtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape.akiihididPaeigk 306
                                       vt tl+GlG++p+++++++gmlGmhGt+ean+++++ad+++a+Garfddrv gn ++f     kiih+didP++i+k
  lcl|FitnessBrowser__PS:Dsui_3529 234 VTNTLMGLGGYPATDKQFVGMLGMHGTYEANMTMQHADVVLAIGARFDDRVIGNPEHFGGVpRKIIHVDIDPSSISK 310
                                       **********************************************************865168************* PP

                         TIGR00118 307 nvkvdipivGdakkvleellkklkee..ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaiv 380
                                        vkvd+pivG++  vl+ellk l +      +   W+++i+ w++++ l +++  + i+Pq+v+++l++++++ea++
  lcl|FitnessBrowser__PS:Dsui_3529 311 RVKVDVPIVGNVPDVLDELLKLLDDGakAAPDVSdWWQQIDGWRAKNSLGYKQ-GDLIEPQYVVEKLYEVTQGEAFI 386
                                       *********************99876543334445************987764.567******************** PP

                         TIGR00118 381 ttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipv 457
                                       t+dvGqhqm+aaq+yk++kpr++i+sgGlGtmG GlP a+G+  a+p ++v ++tG+gs+qm +qelst++++++pv
  lcl|FitnessBrowser__PS:Dsui_3529 387 TSDVGQHQMFAAQYYKFDKPRRWINSGGLGTMGVGLPYAMGVLFANPGAQVACITGEGSIQMCIQELSTCKQFELPV 463
                                       ***************************************************************************** PP

                         TIGR00118 458 kivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldv 532
                                       ki++lnn +lGmv+qWqe+fy++rys+++++s lpdfvklae+yG++g+riekpe++  +lk+a+++   ++v++d+
  lcl|FitnessBrowser__PS:Dsui_3529 464 KIINLNNGMLGMVRQWQEMFYSKRYSQSYVTS-LPDFVKLAESYGHVGMRIEKPEDVVPALKKAFTEYkdRLVFMDF 539
                                       *******************************5.*******************************98654599***** PP

                         TIGR00118 533 evdkeeevlPmvapGagldelvee 556
                                        +d e++v+Pmva G+gl+e++ +
  lcl|FitnessBrowser__PS:Dsui_3529 540 IIDPEANVYPMVAAGKGLSEMILS 563
                                       *********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (566 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis